Over on SciFi Scanner, John Scalzi suggested how to improve the American Film Institute's list of top ten science fiction films. The problem with AFI's list is that it only contains films from 1991 and before. Since there have been a ton of great SF films created in the last 17 years, that's a hell of an oversight.
I agree with all five of Scalzi's additions--The Matrix (1999), Ghost in the Shell (1995), The Incredibles (2004), 12 Monkeys (1995), and Eternal Sunshine of the Spotless Mind (2004). I would also propose the following films: Gattaca (1997), Children of Men (2006), and most importantly, Alex Proyas's masterpiece Dark City (1998). People might also be interested in Cinemension's Great Films List, which breaks the best films down by genre, director, and more.